Hi Madroxide. I see people with this problem often and what works for one may not work for another.
Here are most of the solutions I've found in the past.
Settings > Application Manager > All > Messaging > Clear data.
go to settings> developer options>and uncheck (do not keep activities) this must be unchecked, and also make sure limit background processes is set to standard.
And another..
Go to your message inbox, press the menu key, and go to settings. Look for "Manage SIM card messages", if there are any messages here, delete them. If that does not work, under message settings uncheck notification, and power off the phone for a few minutes.
One more..
Send a message to a landline. You'll get an error popup, open that message and if there is another message inside of it, delete.
Lastly, try
Handcent and disable your stock message app.